Sage Legacy
by Dyn4mic Duo
Summary: What if after the Kyuubi's Attack, Naruto were kidnapped by Orochimaru & experimented on? And what if it results in a Sharingan? The experiment's change him- but no one knows of it's full implications. Now Naruto has grown, under the supervision of Sarutobi and the tutelage of Itachi and thus he must once again embrace his destiny. Sharingan Naruto. Naru/Kure Pairing.
1. Prologue

**A/N:Hey guys its my first try on fan-fiction so i hope you guys would like this story so please be lenient on me. Also guys sorry how it was earlier its my first time so i am having a little problem in uploading but i have fixed it now.  
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**Disclaimer : I do not own Naruto... Yet, but soon he will mine.**

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Hiruzen Sarutobi also known as Kami no shinobi stood bewildered; as he watched the gigantic fox vanish into the body of the little child. The barrier that had been keeping them at bay broke at once, letting them in, and there he stood- looking upon what remained of the Namikaze family. On the floor was the lifeless body of Minato Namikaze, the Yondaime Hokage and next him to him lay Kushina Uzumaki, his beloved wife. And between them, was the little blond boy who was now the new jinchuriki of the Kyuubi.

'So, this is how it ends' he thought, shocked at all that had unfolded so far. A tear dropped from his eyes, looking at the deceased couple. Such a tragedy…. He lifted up the child and looked at him, the child was crying- loud and clear; as though he could truly feel the pain of his parent's death.

"Get an Anbu squad here right now, we need to dispose everything here and get Minato and Kushina out of here to give them a proper burial, this is the top priority at the moment. Understood?"

"Yes, Hokage-sama" answered the the white masked Anbu, hurrying back to the village at high speeds- while the other one stood guard watching over the scene.

'Hokage… I haven't been called that in a long time. It belonged to you, didn't it Minato? You truly earned it and deserved it. You saved the village and died the way a true shinobi should. I will honor you.

He held the boy tightly to his chest and set back towards the village. "I need to get you to the hospital" he whispered as he vanished into the dark of the cold night with the swirl of leaves. Unknown to him a pair of pale yellow eyes watched him go.

"Ku ku ku you will be perfect for my next experiment"

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~A few days later ~

Hiruzen Sarutobi sat at his desk, going through papers- reinstated as Hokage after the death of the Yondaime. He was deep on thinking when all of a sudden, a Anbu barged into the room. He was drenched in sweat and looked fearful with panic. "Hokage-sama", he said bowing, whilst panting. "What is it?" asked Hiruzen suddenly curious looking at the state of the man.

"That child.." he lowered his voice, as he approached Hiruzen. "The Yondaime's son, he's gone sir."

"What do you mean gone?" replied Hiruzen shocked, already forming conspiracy theories in his head.

"He's been taken, sir. We just found three medical ninja's dead, and the child was missing."

"Impossible" he mumbled closing his eyes. None could have known he was the fourth's son. At least not yet. How could it be...?

He finally opened his eyes and issued command. "Alright, Captain. Lead the way; I want to see the scene."

It wasn't long before they finally reached the hospital. It was an old, dull building- long past its prime. It had taken significant damage during the fox attack, and a good number of people had died. Only two kinds of people were present there- there were the ones sobbing and then there were the ones being sobbed over. The place was filled with the stench of medicine and blood, two of which did not quite go well together.

The third Hokage followed at a breakneck pace until they finally arrived in front of a small room on the top floor. The door had been knocked down; its remains still lay untouched crime scene.

The bodies of three shinobi lay on the floor. Two were female and the other was male. There were no marks on them of any sort, surprising as it was- they barely had a scratch on them. Odd Hizuren remarked. The bodies had just begun to smell, so it hadn't been too long since they'd died. He looked upon the bodies once again, inspecting them for something- anything. He turned the head of one of shinobi's, and gasped in shock. Behind her collar, almost barely visible- was a small mark. It was right over her neck, close to the shoulder on the left hand side. It was- a small tattoo. At once Sarutobi let out a breath he'd been holding all along, as he finally came to a conclusion.

Orochimaru.

Without any delay he bit his thumb and start making a series of signs, and placed it on the ground. A strange black seal apparated onto the floor followed by a burst of smoke. The Anbu officer watched with surprise as a big 7 foot monkey erupted out of nowhere.

"Hey, Hiruzen. What's up now? I thought I told you- I need my rest. Especially after that fox fiasco, god knows I could do with some sleep."

"I'm sorry Enma, But I need your help and its very important" He nodded towards the bodies on the floor.

The ape crawled over to the bodies and began examing them.

"Ah", he said all of a sudden, finally stumbling upon the small negligible tattoo. "So, He's back"

"Yes, so it seems" replied Hiruzen, anxiously.

"I always knew that child was wicked. You should have killed him, when you had the chance, Saru. Anyway- I've got the scent. He was careless with this job here. Follow me"

With a swift movement he ran to the window and jumped out head straight. Hiruzen followed suit, with lingering memories of his last encounter with his old student. Perhaps, I should have killed him…but I couldn't…

At first the ape bounded straight out of Konoha, with a perfect sense of direction following a perfect track as though it was hypnotized to walk that way. But after a while he looked disoriented, and lost the path.

"Damn, that Orochimaru. He's good. But I've seen better things in my day. If he thinks his little tricks will stop me, he's got another thing coming."

He roamed around in circles for a while until he finally found the right scent again and set off trotting. A few times, they reached dead ends and well set traps, but they managed to evade all of them, thanks to the ape's keen nose. And before long, they reached the place they'd meant to.

It was a giant cave, leading underground. Hiruzen motioned for the one and only Anbu officer behind him, and commanded him to call for back up. Not so long after he ran off, the ape looked to him.

"You sure about this Saru? You want to go in there alone before reinforcements come?"

"This is Orochimaru we're talking about, he must have sensed us coming - he might already be preparing his escape. I cannot risk losing the fourth's son and the nine tails. I need to go in there and do something. The priority is to get the child to safety. God knows why he's taken the boy and what he's done to him."

"Alright, follow me then." The ape replied still unconvinced.

They went down the murky space of the cave, steeping down carefuly. What had seemed like a cave was actually a well tiled entrance to a large one floored-house. It was all a Genjutsu.

You always loved your jutsu, didn't you Orochimaru? And it is that very desire for it that led you astray. Perhaps I should have seen it, it was there all along. I knew of it- but I'd just refused to acknowledge it. Maybe if I had, I might have been able to do something and just maybe...Maybe…things would have turned out differently.

He dismissed the thoughts; there was no room for such things now. There were bigger priorities here; the child's safety was the foremost. There wasn't much to be seen in the dark space of what seemed to be Orochimaru's temporary residence. It was all rather grim and fowl. Hiruzen blindly followed the ape, trusting his instincts- that would be the fastest way. Looking through each of the rooms present in the cave would have taken much too long by which time Orochimaru would have been long gone.

Finally, as they trekked through the dark- they could see a bright light at the end of the hallway. They ran up to it as fast as they could without giving themselves away. But it was futile, because as they entered silently Orochimaru spoke in his quite snake-like voice.

"Ah, have you come to greet me Sarutobi-sensei ?, Did you miss me? To have found me so quickly despite all my distractions- you still haven't lost your old touch. I am impressed. I thought you'd grown weak and senile after your retirement"

"Where is the boy Orochimaru? What have you done with him?" demanded Hiruzen in a wave of fury.

"Oh, he's here. I was just uh- running some tests" He sneered with a grin on his twisted face, looking towards a big tube filled with a strange green liquid. In it, floating right at the center- was the baby. "But sadly, it seems as though they have failed. The boy will not live even after having Kyuubi in him. A pity, really, he would have been such a perfect specimen in future " He finished.

"OROCHIMARU" screamed a tearful Hiruzen. He had failed the fourth; he had let his legacy die. And it was all his fault. If only he'd been more careful. If only he'd done things right. His life had been nothing but a heap of regrets. But this time, before he passed away- he would set it right. "You will pay for your sins, Orochimaru. I will not leave you. Now I will do what I should've done a long time ago"

"Oops, looks like I've angered you sensei. I'm sorry, I would like to hang back and savor the fun. But I really have to get going. I'm sorry. Another time perhaps?"

Fumes of purple smoke rose out from all directions, and Sarutobi found his senses clouded. It didn't last long, it was only momentary. But by the time he recovered- Orochimaru was gone. All he could here was the distant echoes of his mad laugh emanating. Kukukuku

Hiruzen shouted at Enma to follow Orochimaru and went right to the green tube. He kicked it just hard enough to watch it break and caught the baby safely in his arms. He was a pretty child. With his father's blond hair and blue eyes, and cat like lines lining both his cheeks.

But the baby was not alive. He was not breathing and there was no pulse. No, no. I have failed. I'm responsible. I let the fourth's child die. His parents gave their lives to protect him and I-I failed them both. I made their deaths meaningless. I...

He stopped midway, for a second there he thought he'd felt the baby move. He looked curiously at the boy, begging for it to be true. A second passed, and the baby began crying. He was alive.

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**So guys please review it and fav it. Its an Sharingan Naruto story as i like that type of fan-fic. As for pairing it will be naru/kure. Dont message me to make it Naru/hina as they will be deleted without being read. Also i am having a poll in which team naruto should go So please vote they would be opened till chapter four or five.**

**Ja ne.**

**13/8/2014 Update - Fixed some mistakes.**


	2. Awakening

**A/N: Hey guys sorry for the late update, this chapter got deleted and we had to write it again from scratch again.  
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**Response to reviews,**

**dogsoldier36 - I know bro, i saw it and fixed immediately, it was my first time uploading that's why it somehow came with html coding.**

**Phantom - Genjutsu doesn't require sharingan, people with high chakra control can perform genjutsu like Kurenai.**

**SSJ3 Kyuubi Gohan - Bro i will have them short so that i can update regularly, as i have boards this year- i am rather busy with studies so i am trying my best to write the chapters as long as possible.**

**So now without any further await i hereby present you the chapter.**

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**_DISCLAIMER_: Dang Darkclaw, Kishi ranaway, quick we have to ****capture him, ** we want his Naruto afterall.

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**Monologue:** A few days after the Orochimaru break-in and a week after Kyuubi attack- Funerals had been held for the heroes who gave their life's in the Kyuubi attack; including the funerals of their beloved Yondaime Hokage. Though not quite as well known to others, right next to Yondaime's grave was the grave of his dear wife Kushina Uzumaki.

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**~Council meeting room~**

The Clan heads sat, growing impatient by the second. All of them were present along with the Hidden Leaf's elders and the civilian council-waiting for the Sandaime's arrival. It was then the door opened, revealing the 'kami no shinobi' in his Hokage robes.

He looked old, older and more weary than ever- all his years seem to fall on him at once- yet he walked with a strength that should've been impossible for his weary bones. But then, the room's entire occupants heard a small cry. It was then that they noticed it. Nestled in the old man's arms, was a little baby, about the size of a shoe box. The silence was broken once more when the 3rd Hokage finally spoke, after abruptly shutting the door behind him.

"As we all know, our beloved Yondaime Hokage fell in battle saving our village from the Kyuubi last week. And as per your previous requests- I shall once again become the Hokage of the Hidden Leaf village. And now- as we proceed towards the matter of the Kyuubi. We must discuss certain things about this child." He lifted up the small baby for all to see clearly. The baby in response began crying, much to the displeasure of all those present.

"How does this matter involve the 'child' Hokage-sama" enquired a rather tall council member, who was eyeing the baby as though he were some peculiar object.

"Being one of the nine tailed beasts- the Kyuubi is a mass made up of chakra. Thus, it cannot be slayed."

"But the Yondaime killed it!" objected another council member.

"No, not even Yondaime could kill it- in fact none can. The only way to supress a tailed beast is in fact are- sealing techniques."

"And so Minato sealed the Kyuubi into this boy, didn't he?" interrupted the lazy voice of the Nara clan head- Shikaku.

"Yes, he did." Hokage said gravely, and a silence fell over the room. A minute passed before anyone spoke again.

"That demon should be killed!" burst a Young man, his eyes cold and overcome with fear. Several people nodded in agreement and soon the room was filled with screaming and a lot of shouting. But the gist of their screaming was much the same: To kill the child.

"Kill that demon!" shouted a woman.

"That fox took my family! Kill it!" hollered another man, getting off of his chair.

"SILENCE!" Hiruzen yelled at once- and the noises died down at once. Slowly the voices calmed down and they all looked at to him anxiously. Noo one wanted to face the wrath of the man who'd been once dubbed the god of shinobi, no matter how old or frail he got.

"He is but a child. Just because he has a demon sealed within him, does not make him one. Even now- it is this little boy that is holding back the Kyuubi from running free and wrecking havoc. He is protecting us all."

"But Hokage-sama!" interevened a civilian only to be cut off by the Hokage.

"This boy shall remain alive- that is all. And from now on the fact that this child has the Kyuubi sealed inside him shall remain an an S-class secret. None are to speak of it again after exiting this room. And a law shall be enforced from here on out that- whosoever in anyway speaks of the Kyuubi or anything related to the matter in front of this child shall face a strict punishment that wil be decided depending on the circumstances. Though do not expect anything less than permanent exile and death. The child must grow up just like any other of the Hidden Leaf, he will know nothing of this. Now anymore questions?"

A tall bandaged old man stood up, raising his left arm. He right sight, including his arm was covered in bandages. He had balding grey hair and a scarred face. He looked straight into the Hokage's eyes- seemingly unshaken. A cold silence fell as he spoke, none wished to interrupt the man. Their eyes held great fear, and some even gulped as they watched him talk.

"Hokage-sama, as we discussed yesterday along with the Council of Elders- I agree to all of this. But I would like to remind you of what I said the other day. Grant me the permission to take this child to raise him. I shall train him and turn him into perfect weapon for Konoha. My root division will be the perfect place for him- he will remain under constant observation and grow like a shinobi should. All of this of course will be under strict secrecy."

"No, Danzo. My answer has not changed and never will- you will not have him."

"Then who will take care of the de- I mean the child" inquired a civilian member.

"Yes Hokage-sama, let Danzo-sama take the child and keep him under survelliance. He might become a weapon for us with training and control." said another.

"ENOUGH I am not going to let Danzo have the boy and as to will take care of the child- I will. I will raise him and in time will also train him. Either way he is no nameless child, I happen to know his name. His name is Uzumaki Naruto and from today henceforth he will be a shinobi of the Hidden Leaf Village."

At the mention of his name, the baby began crying loudly only to soothed by the Hiruzen. The boy suddenly grabbed the mans finger with his small hands, laughing at being soothed. For once, since his birth- the boy truly looked happy.

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**~4 years later~**

Four years had passed since the Kyuubi attack and Naruto had shown no abnormality from Orochimaru experiments. He went regular health check ups and tests- but none of them yielded anything. The only thing about him that was anywhere close to abnormal was his high chakra stamina. Though the matter regarding him and the Kyuubi incident had been declared an S- class secret, the whole village had somehow gotten to know of it. In their eyes- he was not a boy but a walking monstrocity. And they spared no chance to let out their hatred at him. Though seemingly they refrained from passing on the knowledge to their young, thus the newer generation knew nothing of the matter- though they mimiced their elders resentment and isolated Naruto.

It was the 10th of October, the day of the Kyuubi festival and also Naruto's birthday. It was a festival held in the honor of all the fallen warriors, celebrating the victory of the Hidden Leaf against the Kyuubi and of it's strong enduring spirit. Amidst all the celebrations a small 4 year old boy with sun kissed blonde hair walked down the road, holding hands with a woman. It was Uzumaki Naruto and his adoptive mother- Eri Sarutobi, the wife of First son of Sandaime.

"Naru-chan are you enjoying" she asked Naruto

"Hai" replied Naruto rather enthusiastically, grinning.

"Come on naru-chan, enjoy it's your birthday after all" she said pushing him forward as they arrived at the carnival area. It was a brimming place full of color and activity. Lines of stalls and stores were spread out everywhere, while people in yukata's walked around- talking, laughing and eating.

Naruto slowly let go of her hand and looked around. He spotted a frog shaped stall and ran for it. It was hard going through the crowd, but being a child Naruto moved mcuh faster than any adult among such crowds. But as he turned around expecting his adoptive-mother Eri Sarutobi, he only found a group of women in yukata's. She wasn't there. He was lost. The sudden realization brought a surge of panic and fear upon him. It was very crowded now, it would be very hard to find his mother. Then a thought struck Naruto. It was beter to get out of the crowd, from there he could search for his mother.

It took a while but finally, Naruto stepped out of the crowd and reached the edge of the festival. Here there were barely any stalls or people, just darkness. The place gave Naruto the creeps. A shiver ran through his spine as a cold wind passed through.

In the distance watching the sight of a lonely boy roaming were 3 chunin's.

"Guys, " one hiccuped. "Look what we've got ourselves on the day of the kyuubi festival- the Kyuubi itself."

"I can't believe that monster still lives! He murdered my father!" said another

"Let's get that brat and teach him a lesson," instigated another. "I've had enough seeing that monster run around free."

They all nodded and muttered comments of agreement as they put aside their sake bottles and went for their cloaks. Then they simultaenously pulled out their kunai's and advanced towards Naruto who was now shivering from fear.

Naruto even at the tender age of 4 knew very well that the whole village hated him. Though he did not know why, no matter how much he thought on it- he never did understand. Everyone went as far as to call him a demon- but how was he a demon?. So as he saw the chunin approaching him with their kunai's drawn and a murderous look in their eyes he did what his instincts told him to do- run.

It was then that Naruto would realize that being a 4 year old had it's limits. He couldn't run anywhere close to the speeds of an adult and even having great stamina didn't sub for his small age and feet. As a few seconds passed and Naruto's breath grew heavier he ended up in dark alleyway. He ran straight ahead without daring to look back, fearful at what he might find. As he approached the darkest part of the alleyway, his eyes finally adjusted to the darkness and he finally saw what lay ahead- a dark long grey wall. It was a dead end.

"Ha! where you will run now demon?" came a voice from behind.

Fear and despair flowed grew in Naruto, but they weren't the only things growing- so was his anger, curiosity and sadness. He was angry more than anything for being treated this way for reasons unknown- it brought him great sadness. And amongst it all the curiosity pressed him to speak his mind.

"Why are you calling me a demon!? What did I do to you?" he asked turning to face the group of people that now stood before him.

"What did you do?" roared a bearded man. "You can fool the Hokage but not us you monster! You're a killer, a demon! You're murdered countless people! people you have killed"

"I haven't killed anyone! What are you talking about!?" replied Naruto, tearful.

"Enough with this act now!" said a tall man, stepping forward. He seemed to be the leader of the men. "We will kill you- like you killed our families, so that they can finally rest in peace. Then we will be praised as heroes for ridding this village of a curse like you!"

He hurled a kunai towards Naruto. Suddenly the time seemed to slow down, as Naruto watched the Kunai speed towards him, it was as if he were watching his death coming towards him- which was probably true in this case. Then all of a sudden everything turned red. From the dark grey walls to the black kunai that was edging towards him- his vision had gone red. As the kunai came ever closer, he tried to move will his strength. But he could only move enough to avoid a fatal blow. As the kunai made contact naruto screamed in pain- the kunai had slashed his shoulder. And to add to that- his eyes were throbbing as well- the overall pain was unbearable and excruciating.

A weasel masked Anbu bent down to pick up his fallen whistle when suddenly he heard a scream in the distance. He quickly performed a shunshin and finally reached the source of the scream. Before him lay the demon boy- Naruto with a bleeding shoulder and hands over his eyes. Towering above him were three chunins with their kunai's out, who looked as though they were ready to pounce. The Anbu quickly blew the whistle and then marched forward. He intervened, standing in between them and pulling out his sword.

"What's happening here?" he inquired, his voice hollow of emotion.

"We were just finishing what the Yondaime started, slaying the Demon Fox." replied a tall man who smelled strongly of sake.

"Yeah and then everyone will hail us as heroes!" said a rather smelly bearded chunin.

"You know that it is forbidden to speak of suck things." He replied again in his emotionless voice.

"You traitors! He's a killer! He is the Kyu-" Before he could complete his sentence the tall man fell to his knees, with a dart sticking out of his neck.

"For breaking the Sandaime laws you are under arrest. I will now take you to the Hokage and the Council of Elders to recieve your punishment. You have the right to remain silent." He glanced at the other two, who were clutching their kunai's firmly and holding them forward. "Anbu never travel alone- I've got two others surrounding the perimeter. They came here when I whistled earlier. Now unless you want to faint like your friend here- drop your weapons and surrender."

At this the men dropped their kunai's and bent down, putting their hands behind their heads. Immediately two masked Anbu members appeared out of nowhere and bound the two- nodding to the Weasel-masked Anbu. The weasel masked man now looked to the boy who was clutching at his eyes, whilst his shoulder bled with blood of crimson red. He cleared his throat and spoke out loud.

"Naruto, what happened- why are you clutching at your eyes?"

"My eyes...they're burning. It hurts!"

Burning! thought the weasel-masked Anbu. "Burning in the eyes... was he turning back into the demon fox? He then tried to recall all his knowledge.

No, he thought Burning in the eys...its a rare phenomenon...it could only mean... He looked at the fallen boy. It couldn't be...

"Naruto, quickly open your eyes! Watch me" He commanded with anxiety apparent in his voice. Since the weasel had joined the Anbu he had been assigned to keep an eye on Naruto and to prevent him from being subject to harm. The Kyuubi attack hadn't done anything to him or his family so he bore no personal grudge and after watching the child for a good number of years- he'd started to like the boy. He was a decent child, normal enough- though isolated and shunned.

"O-Okay" managed Naruto in a low voice.

The boy's eyes slowly opened. His iris's had turned red and two tomoe were present in his right eye, while only one was present in his left. The weasel-masked man couldn't believe it!

"Sharingan" He gasped.

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**So guys please do tell us your opinions, as feedback will only help us improve. Please review it, fav it and follow it. Also polls are still open so please vote in which team you want to see Naruto in.**

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**Also thank you guys for 400 hits in a single chapter, i hope you will be keep supporting us like this.**

**Peace out**

**Ja ne.**


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